JAL-2505 set helix number as feature group in SequenceFeature

[jalview.git] / src / jalview / analysis / Rna.java

diff --git a/src/jalview/analysis/Rna.java b/src/jalview/analysis/Rna.java
index 89c5c30..6bb123a 100644 (file)
--- a/src/jalview/analysis/Rna.java
+++ b/src/jalview/analysis/Rna.java
@@ -31,10 +31,11 @@ import jalview.datamodel.SequenceFeature;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Map;
 import java.util.Stack;
-import java.util.Vector;
 
 public class Rna
 {
@@ -132,11 +133,11 @@ public class Rna
    * @return
    * @throw {@link WUSSParseException}
    */
-  public static Vector<SimpleBP> getSimpleBPs(CharSequence line)
+  protected static List<SimpleBP> getSimpleBPs(CharSequence line)
           throws WUSSParseException
   {
     Hashtable<Character, Stack<Integer>> stacks = new Hashtable<Character, Stack<Integer>>();
-    Vector<SimpleBP> pairs = new Vector<SimpleBP>();
+    List<SimpleBP> pairs = new ArrayList<SimpleBP>();
     int i = 0;
     while (i < line.length())
     {
@@ -195,25 +196,9 @@ public class Rna
     return pairs;
   }
 
-  public static SequenceFeature[] getBasePairs(List<SimpleBP> bps)
-          throws WUSSParseException
-  {
-    SequenceFeature[] outPairs = new SequenceFeature[bps.size()];
-    for (int p = 0; p < bps.size(); p++)
-    {
-      SimpleBP bp = bps.get(p);
-      outPairs[p] = new SequenceFeature("RNA helix", "", "", bp.getBP5(),
-              bp.getBP3(), "");
-    }
-    return outPairs;
-  }
+  
 
-  public static List<SimpleBP> getModeleBP(CharSequence line)
-          throws WUSSParseException
-  {
-    Vector<SimpleBP> bps = getSimpleBPs(line);
-    return new ArrayList<SimpleBP>(bps);
-  }
+  
 
   /**
    * Function to get the end position corresponding to a given start position
@@ -237,23 +222,22 @@ public class Rna
    * @param pairs
    *          Array of SequenceFeature (output from Rna.GetBasePairs)
    */
-  public static void HelixMap(SequenceFeature[] pairs)
+  protected static void computeHelixMap(SequenceFeature[] pairs)
   {
 
     int helix = 0; // Number of helices/current helix
     int lastopen = 0; // Position of last open bracket reviewed
     int lastclose = 9999999; // Position of last close bracket reviewed
-    int i = pairs.length; // Number of pairs
 
     int open; // Position of an open bracket under review
     int close; // Position of a close bracket under review
     int j; // Counter
 
-    Hashtable<Integer, Integer> helices = new Hashtable<Integer, Integer>();
+    Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
     // Keep track of helix number for each position
 
     // Go through each base pair and assign positions a helix
-    for (i = 0; i < pairs.length; i++)
+    for (int i = 0; i < pairs.length; i++)
     {
 
       open = pairs[i].getBegin();
@@ -307,7 +291,6 @@ public class Rna
 
       lastopen = open;
       lastclose = close;
-
     }
   }
 
@@ -500,4 +483,76 @@ public class Rna
       return c;
     }
   }
+
+  public static SequenceFeature[] getHelixMap(CharSequence rnaAnnotation)
+          throws WUSSParseException
+  {
+    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+
+    int helix = 0; // Number of helices/current helix
+    int lastopen = 0; // Position of last open bracket reviewed
+    int lastclose = 9999999; // Position of last close bracket reviewed
+
+    Map<Integer, Integer> helices = new HashMap<Integer, Integer>();
+    // Keep track of helix number for each position
+
+    // Go through each base pair and assign positions a helix
+    List<SimpleBP> bps = getSimpleBPs(rnaAnnotation);
+    for (SimpleBP basePair : bps)
+    {
+      final int open = basePair.getBP5();
+      final int close = basePair.getBP3();
+
+      // System.out.println("open " + open + " close " + close);
+      // System.out.println("lastclose " + lastclose + " lastopen " + lastopen);
+
+      // we're moving from right to left based on closing pair
+      /*
+       * catch things like <<..>>..<<..>> |
+       */
+      if (open > lastclose)
+      {
+        helix++;
+      }
+
+      /*
+       * catch things like <<..<<..>>..<<..>>>> |
+       */
+      int j = bps.size() - 1;
+      while (j >= 0)
+      {
+        int popen = bps.get(j).getBP5();
+
+        // System.out.println("j " + j + " popen " + popen + " lastopen "
+        // +lastopen + " open " + open);
+        if ((popen < lastopen) && (popen > open))
+        {
+          if (helices.containsValue(popen)
+                  && ((helices.get(popen)) == helix))
+          {
+            continue;
+          }
+          else
+          {
+            helix++;
+            break;
+          }
+        }
+        j -= 1;
+      }
+
+      // Put positions and helix information into the hashtable
+      helices.put(open, helix);
+      helices.put(close, helix);
+
+      // Record helix as featuregroup
+      result.add(new SequenceFeature("RNA helix", "", "", open, close,
+              String.valueOf(helix)));
+
+      lastopen = open;
+      lastclose = close;
+    }
+
+    return result.toArray(new SequenceFeature[result.size()]);
+  }
 }